Influenza Virus Mashup

(Tue, 29 Dec 2009 12:12:00 +0000)

# 4198

Two unrelated stories, except that they involve farm animals in South Korea infected with two very different influenza viruses; one human adapted, and one low-path avian.

While neither story is particularly alarming, they do illustrate how difficult it is to keep human and avian flu strains out of domesticated livestock.   

South Korea tests livestock more rigorously than many other nations, and understandably reports these sorts of infections more often than many other countries.   It is pretty safe to assume that similar infections are going unreported in many places around the world.

Number of H1N1 Infections Growing on Pig Farms

SEOUL, SOUTH KOREA - South Korea reported today another case of H1N1 infection at a local swine farm, adding to a growing list of pigs infected with the flu, local media reported.

 

The latest outbreak occurred in a pig farm in Jeungup, Jeolla Province, marking the sixteenth confirmed case of H1N1 infection since mid-December when five farms reported infection for the first time in the country, according to local media.

 

Authorities are suspecting pigs in the latest case might have contracted the virus through human contacts and expecting them to be naturally cured, according to media reports.

 

The country’s farm ministry plans to take quarantine measures and vaccinate hog industry and health workers in an effort to stem further spread, local media said.

Low path H5 and H7 viruses are reportable animal diseases, even though they pose little health hazards to humans.   Low pathogenic viruses have the potential to mutate into highly pathogenic viruses, therefore their appearance is taken seriously.

S. Korea: Low pathogenic H5N2 in ducks

29 Dec 2009

On a duck farm in South Korea low pathogenic bird flu type H5N2 has been diagnosed.

 

The duck farm in Chung Chong-Namdo (Gobuk-myeon, Seo-san city) holds 26,800 duck of which 40 birds were found to be positive for H5N2. The source of the infection could not be established.

 

As part of the yearly surveillance programme, a member of the Livestock Health Control Association collected samples from a duck raising farm in Seo-san city and requested the test for avian influenza to the Chungchong-namdo Veterinary Research Institute (VRI) on 7 December 2009.

 

<SNIP>

26,800 ducks raised in the affected farm were culled and 176,000 eggs kept in the farm were destroyed.

(Tue, 29 Dec 2009 11:26:00 +0000)

# 4197

Given that none of the pandemics of the 20th century were over in less than a year, it is hardly surprising that the Director-General of the WHO (World Health Organization) - Margaret Chan - is unwilling to declare victory now that the virus appears to be receding in North America and and parts of Europe.

It isn’t lost on scientists that in 1957, the Asian Flu pandemic seemed to disappear completely for more than a year, only to return in 1959 and again after a two year lull during the 1962-63 flu season.  

 

 

NEJM 2009

Today, Director General Chan stated that it will take another 6 months to a year to know if this pandemic is truly on the wane, and she reminds us that we are not ready for a more severe H5N1 pandemic.

This report from AFP.

WHO chief says too early to declare flu victory

December 29, 2009 - 8:59PM

World Health Organisation chief Margaret Chan said Tuesday it was too early to declare victory over swine flu and insisted that measures taken to deal with the pandemic were justified.

 

“I think that we must remain prudent and observe the evolution of the pandemic over the next six to 12 months before declaring victory,” she told Swiss newspaper Le Temps in an interview.

 

Even though the peak of the flu has passed in some countries of the northern hemisphere, such as Canada and the United States, others countries were far from seeing the end, she noted.

 

“Winter is still long,” said the WHO director-general, adding that a precise picture of the flu’s impact would not be seen before two years.

 

 

(Continue . . . )

I’ve just added a new blog to the Influenza: español list: Influenza A en Venezuela. Its latest post: Casos confirmados de Gripe AH1N1 en Venezuela. [Confirmed cases of H1N1 in Venezuela]

The table from the Directorate of Epidemiological Surveillance says that 2,742 H1N1 cases have been confirmed, and 2,235 cases have been “de alta epidemiologia”–which I take to mean cases requiring intensive care. And 121 of the confirmed cases have resulted in death.

That looks like a 4.4 percent case fatality ratio, far higher than most countries have reported. More likely, they’re testing only the critically ill, and a huge number of Venezuelan H1N1 cases have gone unnoticed, undiagnosed, and unreported.

Via The Kathmandu Post: Government confirms swine flu deaths. Excerpt:

The government on Monday confirmed that swine flu has killed two people in the country so far. 

This came a day after reports of the first-ever swine flu death in the country.  

The Department of Health Services under the Ministry of Health (MoH) said in a press release that a 31-year-old woman from Chitwan had died at a hospital on Dec. 5. Another 29-year-old woman, who had renal failure, died in  course of treatment on Dec. 24. 

According to World Health Organisation (WHO) estimates, which declared a swine flu pandemic on June 11, the disease has killed over 11,500 people worldwide, including over 850 in India. 

In Nepal, swine flu cases were reported six months ago. The first confirmed cases were three Non-Resident Nepalis of a family, who had arrived in Kathmandu from the US via Qatar on June 29. 

The MoH stated that it had confirmed 150 swine flu cases in the country as of Monday. It said the patients—106 males and 44 females—were aged between 15 and 45 years.

The statistics in the last paragraph are surprising: H1N1 usually afflicts males and females equally. I would guess that a large number of female cases are going unnoticed and untreated.

(Mon, 28 Dec 2009 18:33:00 +0000)

# 4196

The ECDC (European Centre For Disease Prevention & Control) like many agencies, took some time off last week and did not issue any daily reports on Thursday and Friday.  So today’s update covers the events of the past 5 days.

 

Main developments in the past 5 days

Weekly Influenza Surveillance Overview published December 24th and covering Week 51 (Dec 14th  to 20th) found that most reporting countries were observing declining trends with the most reported influenza activity being in South Eastern Europe

 

A total of 1 803 fatal cases in Europe and EFTA countries and 10 879 in the rest of the world have been reported up to date. 

 

ECDC published a summary on the D222G/D222N mutations in the pandemic virus

Perhaps of most interest is the latest report on the D222G/D222N mutations in the pandemic virus.

While the ECDC believes that further study of these mutations and surveillance is warranted, they believe that as of right now, they should have a minimal impact on public health and pandemic response.

They find no direct evidence that these mutations are responsible for an increase in virulence (although they leave that door open a bit), or that they are being transmitted easily.

Here is the ECDC summary, and a more complete report is available here.

(slightly reformatted for readability).

ECDC Summary on Pandemic 2009 Virus Mutation D222G/D222N published in its Public Health Developments Series 

December 23rd

Recently, several countries have reported finding mutations of the 2009 pandemic virus. One particular mutation has come to attention, especially following a formal notification by Norway through the International Health Regulations and  Early Warning and Response System  reporting mechanisms.(1)

 

The particular  change a substitutions in a specific codon of the Haemagglutinin (HA) gene and is called either D222G and D222N depending on the precise change. The variants have been especially found in a number of severe cases of pandemic influenza including deaths and it has been suggested that the variants could cause more efficient infection of deeper airways resulting in a more serious disease profile.

 

No direct evidence for this exists and cases have also been found in mild infections. The D222G and D222N variants, and sometimes mixtures thereof have been described in viruses and sequences derived directly from clinical specimens of 2009 pandemic influenza A(H1N1)  cases in at least 20 countries, including Brazil, China, France, Italy, Japan, Mexico, Norway, Spain, the Ukraine and the USA.

 

These mutations are not new in this pandemic, they have been found in cased going back to April 2009.

 

To date no connection between cases, suggestive of transmission, has been found and it seems that the appearance in various countries is more the result of routine sequencing rather than spread of the mutation.  It is also unclear if the association with severe cases is coincidental or not, perhaps resulting from preferred sequencing of specimens and viruses from severe cases/deaths.

 

After considering the current available virological, epidemiological and clinical findings and following discussions on an earlier draft with WHO and its European-based Collaborating Centre ECDC has come to a preliminary formulation namely that the G222D/N variants exist in a small proportion of  sporadic severe, as well as mild cases of 2009 pandemic  influenza A(H1N1) infection and that these represents natural variation of the virus with no special association with severity of the disease course.

 

As such and while they do not transmit they should have a minimal impact on public health and pandemic response. Current data suggests that the cases involving variant viruses in different parts of the world are unrelated and the underlying mutation events probably occurred independently from each other in the infected individuals as a consequence of the natural variability of influenza viruses and their inability to correct random coding errors.

 

However because of that inherent variability and  ability to surprise the 2009 A(H1N1) will need on-going combined virological, epidemiological and clinical surveillance and study.(2)

1.  WHO Pandemic (H1N1) 2009 briefing note 17.
http://www.who.int/csr/disease/swineflu/notes/briefing_20091120/en/index.html

2.  ECDC 2009 pandemic influenza A(H1N1) virus mutations reported to be associated with severe disease ECDC Public Health development December 23rd  2009

I’ve just spent some time cleaning up three lists: H1N1 Resources, H5N1/H1N1 Hot Zone Sources, and H5N1/H1N1 Bloggers. The items I’ve removed are links I rarely or never use.

The dropped sources are mostly newspapers or other media sites in countries where H1N1 has ceased to make news. No doubt as the austral summer approaches, I’ll restore some Australian and New Zealand sites.

Dropping some of the bloggers has been painful–I admire anyone with the interest and desire to cover this story. But some of them haven’t been updated in months, and others are just not useful for my purposes.

As time permits, I’ll review the other lists on this site and drop anything that seems no longer relevant. And of course I’ll add new links if they’re useful. (I’ve just added Influenza Digest, a very good revision of a US government site–it’s in the H1N1 Resources list.)

If I’ve removed a link that you find convenient, let me know and I’ll put it back. And if you can recommend new links, I’ll be glad to hear about them.

Via Egypt News: Egypt death toll of A/H1N1 flu reaches 112. But the headline’s wrong. Excerpt:

The Egyptian the Health Ministry announced on Monday that Egypt reported three more death cases of influenza A/H1N1, bringing the nationwide death toll to 109. 

Egypt’s Ministry said that a 61-year-old man in Cairo, another 40-year-old man and 34-year-old man in Giza died of A/H1N1 virus. 

The Ministry added that up till now, Egypt has reported more than 10,056 cases of the novel flu.

My last report on Egypt, on December 25, gives the Egyptian death toll as 106.

(Mon, 28 Dec 2009 13:49:00 +0000)

# 4195

Even though the pandemic of 2009 continues, and we don’t yet know how it will turn out, there are other infectious disease threats on the horizon. 

Some are flu-related, and others stem from other pathogens.   Some have pandemic potential, while others (right now) are only capable of localized outbreaks.

Either way, infectious diseases – once believed on the way to eradication – are on the comeback trail.

TB (Tuberculosis) was a scourge here in the US 60 years ago.  My Grandmother had it – and was in a sanitarium for months – back in the 1930s. 

When I was a young paramedic, we often saw TB patients.  In fact, I transported TB patients to the Lantana TB hospital mentioned in the article below, back in the 1970s.

Gradually, though, TB here in the US receded in the face of new antibiotics, and improved treatment regimens.   By the late 1970s, most of the TB hospitals had been shuttered, and many believed the disease would soon be eliminated – at least in the developed world.

Of course, that didn’t happen.  TB has learned to evade our first line antibiotics, and in some cases, is becoming to resistant to our higher tier treatments as well.

Yesterday the AP (Associated Press) ran a detailed story about the discovery, and treatment of the first known case of XXDR-TB (Extremely Drug Resistant TB) here in the US.  

The story, by Martha Mendoza and Margie Mason is well worth reading.

Danger at home: Rare form of TB comes to U.S.

First U.S. case of extremely drug-resistant strain of tuberculosis diagnosed

While still incredibly rare, many scientists fear this is the future of TB; increasingly drug resistant and difficult to treat.

An excerpt from the AP report.  But follow the link above to read it in its entirety.

Forty years ago, the world thought it had conquered TB and any number of other diseases through the new wonder drugs: antibiotics. U.S. Surgeon General William H. Stewart announced it was “time to close the book on infectious diseases and declare the war against pestilence won.”

 

Today, all the leading killer infectious diseases on the planet — TB, malaria and HIV among them — are mutating at an alarming rate, hitchhiking their way in and out of countries. The reason: overuse and misuse of the very drugs that were supposed to save us.

 

Just as the drugs were a manmade solution to dangerous illness, the problem with them is also manmade. It is fueled worldwide by everything from counterfeit drugmakers to the unintended consequences of giving drugs to the poor without properly monitoring their treatment. Here’s what the AP found:

• In Cambodia, scientists have confirmed the emergence of a new drug-resistant form of malaria, threatening the only treatment left to fight a disease that already kills 1 million people a year.
• In Africa, new and harder to treat strains of HIV are being detected in about 5 percent of new patients. HIV drug resistance rates have shot up to as high as 30 percent worldwide.
• In the U.S., drug-resistant infections killed more than 65,000 people last year — more than prostate and breast cancer combined. More than 19,000 people died from a staph infection alone that has been eliminated in Norway, where antibiotics are stringently limited.

“Drug resistance is starting to be a very big problem. In the past, people stopped worrying about TB and it came roaring back. We need to make sure that doesn’t happen again,” said Dr. Thomas Frieden, director of the U.S. Centers for Disease Control and Prevention, who was himself infected with tuberculosis while caring for drug-resistant patients at a New York clinic in the early ’90s. “We are all connected by the air we breathe, and that is why this must be everyone’s problem.”

More than 2 1/2 years ago I wrote a blog entitled It Isn’t Just Bird Flu, where I wrote about a number of possible pandemic and epidemic threats.   I opened with:

In this increasingly crowded world of ours, where there are large areas of poverty and poor medical care, there are literally scores of deadly pathogens that could spark the next epidemic, or pandemic.    Bird flu, or the H5N1 virus, is high on the list of diseases we watch, but it is by no means the only one out there.

 

When we prepare for a bird flu pandemic, we are also preparing for any other disease outbreak.

Recently I updated that blog with another called It Isn’t Just Swine Flu.   The message remains the same.  We live in a world teeming with pathogens, many of which are continually changing and evolving to become more efficient at infecting their hosts.

In  October of 2008  Lloyd’s issued a pandemic impact report for the Insurance industry, which can be downloaded here.

The Lloyds report takes pains to point out that while we worry about an influenza pandemic the most, there are other candidates out there that could spark a pandemic (or at least an epidemic).

They list:

• Hendra Virus
• Nipah Virus
• Cholera
• Small Pox
• HIV/AIDS
• Bubonic Plague
• Tuberculosis
• Lassa fever
• Rift Valley fever
• Marburg virus
• Ebola virus
• Bolivian hemorrhagic fever
• MRSA
• SARS

I could add Dengue, Chikungunya, and of course Pathogen X, the one we don’t know about yet, to this list.

While I can’t tell you which of these threats will end up being the big disease story of 2010, I can assure you there will be plenty of pathogen related news to write about and discuss in the upcoming year.

That’s the thing about blogging about emerging infectious diseases.

Despite the premature proclamation of U.S. Surgeon General William H. Stewart back in 1969.  

It’s a growth industry.

(Mon, 28 Dec 2009 12:42:00 +0000)

# 4194

Continuing an experiment today.

 

Since the holidays are upon us and the number of news stories is relatively low, for the next few weeks I will attempt to do a weekly recap of some of the biggest stories, the best blog posts, and most interesting information from Flublogia each Sunday or Monday Morning.

 

This will be a subjective list of things that caught my eye, and is by no means intended to recap all of the news reports or mention every worthy blog post out there.  It is more of a sampling.

 

My apologies for the good stories I may miss.  In no particularly order . . .

On Vincent Racaniello’s  Virology Blog we get an assessment of the efficacy of Tamiflu in the wake of a BMJ article (see BMJ: A Review Of Tamiflu’s Efficacy Against Seasonal Influenza) questioning its usefulness. 

In Influenza neuraminidase inhibitors work, Professor Racaniello gives us the results of a human study published nearly a decade ago that support the usefulness of the drug against influenza.

Also from Vincent Racaniello, the 63rd installment of TWiV (This week in Virology) Podcast.  A fascinating stroll through the world of virology each week.  Highly recommended for disease geeks everywhere.

From the Reveres at Effect Measure a pair of flu-related blogs to note.   First, an excellent overview of the the experimental antiviral being tested in Japan called T-705 – which while still a long way from being on your pharmacy shelves – shows serious promise.

In  A new front line drug for flu in the offing?  Revere gives us a good deal of background information on drug which is about to begin human trials.

Also, in CDC’s 2009 flu wrap up presser  Revere takes a look at the CDC’s last flu press conference, and looks ahead to what might happen this spring.

Maryn McKenna, on her Superbug Blog, makes an important appeal to her readers to help support ProMed Mail, something I heartily endorse as well.   In  A plea, and not for me: Support ProMED she reminds us of the important – donation supported – work done 24/7 by the editors of ProMail Med.

We are all eagerly awaiting the publication of Maryn’s new book Superbug: The Fatal Menace of MRSA (Hardcover) in March.  In the meantime, her excellent MRSA blog  Superbug is now available on Kindle.

CIDRAP News provides excellent coverage and analysis of H1N1 and other disease news, and Mayrn McKenna’s report H1N1 poses grave risk to pregnant women, new moms is a perfect example.   You’ll find additional terrific reporting from CIDRAP by Lisa Schnirring and Robert Roos.

Crof over at Crofsblog, not only keeps the best tabs on the daily news of the pandemic (along with other flu issues), but also writes terrific commentary from time to time as well.   His Blogging H1N1: Lessons so far is a prime example.

Crof may be the hardest working blogger in FluBlogia, and his translations of Spanish Language articles from Mexico and South America are our best window into what is going on in that part of the world.

Chen Qi continues to provide a terrific newspaper-style blog of Flu and Emerging Infectious disease news.  One of the most readable sources of information – gleaned from all over the world – on the next.

As a blogger, I am highly dependent upon journalists who cover the `flu beat’, and while there are many excellent reporters out there, two probably show up on these pages more than any others.

Helen Branswell of the Canadian Press and Maggie Fox of Reuters.

Why?   Because they understand the science, and I trust them to get the story right.

A few examples of the reports these two reporters have recently filed, all of which I used as fodder for this blog.

H1N1 flu virus voted top news story of 2009 in Canadian Press survey  - Branswell

Experts say pandemic could have a silver lining if it knocks out other viruses – Branswell

Other viruses abound in U.S. flu season, tests show - Fox

New Japanese flu drug protects mice from avian flu – Fox

My thanks to both of you, and to many of your colleagues, for the hard work you are doing getting the latest pandemic information out. 

Now is a good time to remind my readers that agencies like the Red Cross, Red Crescent, CARE, Save The Children, The H2P Project, UNICEF, and others are working around the world every day to combat poverty and disease, and are on the front lines every day.

 

They could use your support.

 

These NGO’s do a great deal with very little, and even small donations can help make a difference.   You can find their websites and blogs in my sidebar.

I am somewhat chagrined to admit that it has only been recently that I’ve become a regular visitor to  Mystery Rays From Outer Space, a fascinating blog by assistant professor of immunology and virology at Michigan State University, Ian York, Ph. D.

I am thoroughly enjoying going through the Mystery Rays archives, while wondering how I could have gone this long without discovering this resource.

As always, I am heavily reliant on the newshounds on the flu forums (I frequent Flu Wiki and FluTrackers) which continue to provide the best stream of raw news and information on emerging infectious diseases from around the world.  

As for my own blogging over this past short holiday week, in addition to covering influenza and disease news, a few of my more in-depth blogs included:

Another H9 Report From Hong Kong

Cytokine Storm Warnings

Enough To Make You ILI

US: Dog Tests Positive For H1N1

All of this represents just a sampling of this week in Flublogia.  As you can see, this is a collaborative effort. No one reporter, blogger, or flu forum could cover it all. 

Hopefully this recap will highlight some of the stories you may have missed over the past week.

There are a lot of terrific bloggers, flu forums, agencies, and organizations from around the world who contribute to Flublogia each and every week. 

You can find a lot of them in my sidebar.

It is worth the time to explore these resources, and go back through their archives, looking for dusty, but no-less-valuable gems of writing.